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- PDB-2pp0: Crystal structure of L-talarate/galactarate dehydratase from Salm... -

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Basic information

Entry
Database: PDB / ID: 2pp0
TitleCrystal structure of L-talarate/galactarate dehydratase from Salmonella typhimurium LT2
ComponentsL-talarate/Galactarate Dehydratase
KeywordsLYASE / Enolase superfamily / L-talarate/Galactarate Dehydratase
Function / homology
Function and homology information


L-talarate dehydratase / L-altrarate catabolic process / L-altrarate dehydratase activity / galactarate dehydratase / galactarate catabolic process / galactarate dehydratase activity / amino acid catabolic process / hydro-lyase activity / carbohydrate catabolic process / magnesium ion binding
Similarity search - Function
L-talarate/galactarate dehydratase / Mandelate racemase / muconate lactonizing enzyme family signature 2. / : / Mandelate racemase/muconate lactonizing enzyme, conserved site / Mandelate racemase/muconate lactonizing enzyme, N-terminal domain / Mandelate racemase / muconate lactonizing enzyme, N-terminal domain / Mandelate racemase/muconate lactonizing enzyme, C-terminal / Mandelate racemase / muconate lactonizing enzyme, C-terminal domain / Enolase C-terminal domain-like / Enolase C-terminal domain-like ...L-talarate/galactarate dehydratase / Mandelate racemase / muconate lactonizing enzyme family signature 2. / : / Mandelate racemase/muconate lactonizing enzyme, conserved site / Mandelate racemase/muconate lactonizing enzyme, N-terminal domain / Mandelate racemase / muconate lactonizing enzyme, N-terminal domain / Mandelate racemase/muconate lactonizing enzyme, C-terminal / Mandelate racemase / muconate lactonizing enzyme, C-terminal domain / Enolase C-terminal domain-like / Enolase C-terminal domain-like / Enolase-like C-terminal domain / Enolase-like, N-terminal domain / Enolase-like, N-terminal / Enolase-like, C-terminal domain superfamily / Enolase-like; domain 1 / TIM Barrel / Alpha-Beta Barrel / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
L-talarate/galactarate dehydratase
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsFedorov, A.A. / Fedorov, E.V. / Yew, W.S. / Gerlt, J.A. / Almo, S.C.
CitationJournal: Biochemistry / Year: 2007
Title: Evolution of enzymatic activities in the enolase superfamily: L-talarate/galactarate dehydratase from Salmonella typhimurium LT2.
Authors: Yew, W.S. / Fedorov, A.A. / Fedorov, E.V. / Almo, S.C. / Gerlt, J.A.
History
DepositionApr 27, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: L-talarate/Galactarate Dehydratase
B: L-talarate/Galactarate Dehydratase
C: L-talarate/Galactarate Dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,5236
Polymers132,2473
Non-polymers2763
Water7,728429
1
B: L-talarate/Galactarate Dehydratase
C: L-talarate/Galactarate Dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,3494
Polymers88,1642
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6420 Å2
ΔGint-22 kcal/mol
Surface area27930 Å2
MethodPISA
2
A: L-talarate/Galactarate Dehydratase
hetero molecules

A: L-talarate/Galactarate Dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,3494
Polymers88,1642
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_556-x,y,-z+11
Buried area6530 Å2
ΔGint-17 kcal/mol
Surface area27560 Å2
MethodPISA
3
B: L-talarate/Galactarate Dehydratase
C: L-talarate/Galactarate Dehydratase
hetero molecules

B: L-talarate/Galactarate Dehydratase
C: L-talarate/Galactarate Dehydratase
hetero molecules

B: L-talarate/Galactarate Dehydratase
C: L-talarate/Galactarate Dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)265,04612
Polymers264,4936
Non-polymers5536
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation6_565x,-y+1,-z1
Buried area43060 Å2
ΔGint-106 kcal/mol
Surface area94330 Å2
MethodPISA
4
A: L-talarate/Galactarate Dehydratase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)265,04612
Polymers264,4936
Non-polymers5536
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
crystal symmetry operation5_556-x,y,-z+11
crystal symmetry operation7_556y,x,-z+11
crystal symmetry operation8_556-y,-x,-z+11
Buried area43760 Å2
ΔGint-81 kcal/mol
Surface area92580 Å2
MethodPISA
5
A: L-talarate/Galactarate Dehydratase
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)353,39516
Polymers352,6588
Non-polymers7378
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
crystal symmetry operation5_556-x,y,-z+11
crystal symmetry operation6_556x,-y,-z+11
crystal symmetry operation7_556y,x,-z+11
crystal symmetry operation8_556-y,-x,-z+11
MethodPQS
6
B: L-talarate/Galactarate Dehydratase
C: L-talarate/Galactarate Dehydratase
hetero molecules

B: L-talarate/Galactarate Dehydratase
C: L-talarate/Galactarate Dehydratase
hetero molecules

B: L-talarate/Galactarate Dehydratase
C: L-talarate/Galactarate Dehydratase
hetero molecules

B: L-talarate/Galactarate Dehydratase
C: L-talarate/Galactarate Dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)353,39516
Polymers352,6588
Non-polymers7378
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation5_555-x,y,-z1
crystal symmetry operation6_565x,-y+1,-z1
MethodPQS
Unit cell
Length a, b, c (Å)173.888, 173.888, 123.199
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number89
Space group name H-MP422
Components on special symmetry positions
IDModelComponents
11C-720-

HOH

DetailsThe biological assembly is a dimer

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Components

#1: Protein L-talarate/Galactarate Dehydratase


Mass: 44082.246 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q8ZL58
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 429 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.52 Å3/Da / Density % sol: 65.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 1.6 M AmS, 0.1 M Tris HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 27, 2006
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.2→25 Å / Num. all: 86423 / Num. obs: 86423 / % possible obs: 90.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Biso Wilson estimate: 21.8 Å2 / Rmerge(I) obs: 0.056

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Processing

Software
NameVersionClassification
CNS1.1refinement
ADSCQuantumdata collection
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→24.87 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 261597.65 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.223 4383 5.1 %RANDOM
Rwork0.207 ---
all0.209 86423 --
obs0.209 86423 90.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.9897 Å2 / ksol: 0.367005 e/Å3
Displacement parametersBiso mean: 33.3 Å2
Baniso -1Baniso -2Baniso -3
1-3.97 Å20 Å20 Å2
2--3.97 Å20 Å2
3----7.95 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 2.2→24.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9243 0 18 429 9690
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.6
X-RAY DIFFRACTIONc_improper_angle_d0.82
X-RAY DIFFRACTIONc_mcbond_it1.131.5
X-RAY DIFFRACTIONc_mcangle_it1.612
X-RAY DIFFRACTIONc_scbond_it2.012
X-RAY DIFFRACTIONc_scangle_it2.732.5
LS refinement shellResolution: 2.2→2.28 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.257 416 5.3 %
Rwork0.226 7452 -
obs--83.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4GOL_xplor_par.txtGOL_xplor_top.txt
X-RAY DIFFRACTION5&_1_PARAMETER_INFILE_5&_1_TOPOLOGY_INFILE_5

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